Surprise. I just had "(Unknown)" show up in the battery usage on my Nexus 5 for the first time ever. I was monitoring battery usage a lot lately (due to Wear issues). It appeared perhaps immediately after I performed a Google Play Store update that updated the following apps:
8sms
firefox
rocket player
tivo
wikipedia
And of those, the only one I have launched since the update was 8sms (and they unfortunately added "ads", barf). Anyway, same symptoms as others report- there is no "Unknown" app installed. I can't get any info about "Unknown", I can't stop "Unknown" because there are no options for it, nothing shows up as "Unknown" under running apps. Phone is not rooted.
Doesn't seem like this something that Android should allow to happen.